Alignments for a candidate for trpD_2 in Paraburkholderia bryophila 376MFSha3.1

GapMind for Amino acid biosynthesis

Alignments for a candidate for trpD_2 in Paraburkholderia bryophila 376MFSha3.1

Align Anthranilate phosphoribosyltransferase; EC 2.4.2.18 (characterized)
to candidate H281DRAFT_05713 H281DRAFT_05713 anthranilate phosphoribosyltransferase

Query= SwissProt::Q8PD71
         (345 letters)



>FitnessBrowser__Burk376:H281DRAFT_05713
          Length = 343

 Score =  498 bits (1281), Expect = e-145
 Identities = 253/340 (74%), Positives = 286/340 (84%)

Query: 1   MPITPQQALQRTIEHREIFHDEMVDLMRQIMRGEVSDAMVSAILTGLRVKKETIGEIAGA 60
           M ITPQ+ALQRTIEHREIFHDEM+ LMR IMRGE+S  M +AI+TGLRVKKETIGEI  A
Sbjct: 1   MTITPQEALQRTIEHREIFHDEMLHLMRLIMRGELSPVMAAAIITGLRVKKETIGEITAA 60

Query: 61  ATVMREFSRRVEVTDRRHMVDIVGTGGDGSHTFNISTCAMFVAAAGGAKVAKHGNRSVSS 120
           ATVMREF+R VEV D  + VDIVGTGGDGSHTFNIST  MFV+AA GAKVAKHGNR VSS
Sbjct: 61  ATVMREFARHVEVQDNSNFVDIVGTGGDGSHTFNISTATMFVSAAAGAKVAKHGNRGVSS 120

Query: 121 KSGSADALEALGAVIELQPEQVAASLAQTGIGFMYAPVHHPAMKVVAPVRREMGVRTIFN 180
           KSGSAD LEALG  I+LQPEQVAAS+A+TG+GFM+AP HHPAMK +APVRRE+GVRTIFN
Sbjct: 121 KSGSADVLEALGVNIDLQPEQVAASIAETGMGFMFAPNHHPAMKNIAPVRRELGVRTIFN 180

Query: 181 ILGPLTNPAGSPNILMGVFHPDLVGIQARVLQELGAERALVVWGRDGMDELSLGAGTLVG 240
           ILGPLTNPAG+PN LMGVFH DLVGIQ RV+Q LGA+  LVV+G DGMDE+SLGA T VG
Sbjct: 181 ILGPLTNPAGAPNQLMGVFHADLVGIQVRVMQRLGAKHVLVVYGMDGMDEVSLGAATQVG 240

Query: 241 ELRDGQVHEYEVHPEDFGIAMSASRNLKVADAAESRAMLLQVLDNVPGPALDIVALNAGA 300
           ELRDG+V EYE+HPEDFG+ M ++R LKVADA ES+AMLL+ LDN PG A +IV LNAG 
Sbjct: 241 ELRDGEVREYEIHPEDFGMQMVSNRTLKVADATESKAMLLEALDNKPGVAREIVTLNAGT 300

Query: 301 ALYVAGVADSIADGIVRARQVLADGSARACLDAYVAFTQQ 340
           ALY A VA SIA+GI  AR+ +A G ARA +D  + FTQQ
Sbjct: 301 ALYSANVASSIANGIELAREAIASGKARAKVDELIRFTQQ 340


Lambda     K      H
   0.320    0.134    0.377 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 411
Number of extensions: 7
Number of successful extensions: 1
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 345
Length of database: 343
Length adjustment: 29
Effective length of query: 316
Effective length of database: 314
Effective search space:    99224
Effective search space used:    99224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate H281DRAFT_05713 H281DRAFT_05713 (anthranilate phosphoribosyltransferase)
to HMM TIGR01245 (trpD: anthranilate phosphoribosyltransferase (EC 2.4.2.18))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.aa/TIGR01245.hmm
# target sequence database:        /tmp/gapView.1105.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01245  [M=330]
Accession:   TIGR01245
Description: trpD: anthranilate phosphoribosyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                    Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     1e-129  418.5   6.0   1.2e-129  418.4   6.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_05713  H281DRAFT_05713 anthranilate pho


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_05713  H281DRAFT_05713 anthranilate phosphoribosyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  418.4   6.0  1.2e-129  1.2e-129       1     329 [.       9     336 ..       9     337 .. 0.99

  Alignments for each domain:
  == domain 1  score: 418.4 bits;  conditional E-value: 1.2e-129
                                    TIGR01245   1 leklldnkdLseeeaeqlmkeimsgeasdaqiaAilvalrvkgeteeeiaglakalrekakkveke 66 
                                                  l++ ++++++ ++e+ +lm+ im+ge+s++  aAi++ lrvk et+ ei+++a+++re a++ve++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05713   9 LQRTIEHREIFHDEMLHLMRLIMRGELSPVMAAAIITGLRVKKETIGEITAAATVMREFARHVEVQ 74 
                                                  578999************************************************************ PP

                                    TIGR01245  67 eseelvDivGTGGDglktiNiSTasalvaaaaGvkvaKhGnrsvssksGsaDvLealgvnlelspe 132
                                                  +++++vDivGTGGDg++t+NiSTa+++v aaaG+kvaKhGnr vssksGsaDvLealgvn++l+pe
  lcl|FitnessBrowser__Burk376:H281DRAFT_05713  75 DNSNFVDIVGTGGDGSHTFNISTATMFVSAAAGAKVAKHGNRGVSSKSGSADVLEALGVNIDLQPE 140
                                                  ****************************************************************** PP

                                    TIGR01245 133 kvarsleevgigFlfAPkyhpalkevapvRkeLgvrtvfNlLGPLlnParaklqvlGvyskdlvev 198
                                                  +va+s++e+g+gF+fAP++hpa+k++apvR+eLgvrt+fN+LGPL+nPa a++q++Gv+++dlv +
  lcl|FitnessBrowser__Burk376:H281DRAFT_05713 141 QVAASIAETGMGFMFAPNHHPAMKNIAPVRRELGVRTIFNILGPLTNPAGAPNQLMGVFHADLVGI 206
                                                  ****************************************************************** PP

                                    TIGR01245 199 laevlknlgvkralvvhgedglDEisltgetkvaelkdgeieeytlspedfglkraeleelkggsa 264
                                                   ++v+++lg+k++lvv g dg+DE+sl + t+v el+dge++ey+++pedfg+++ + + lk+++a
  lcl|FitnessBrowser__Burk376:H281DRAFT_05713 207 QVRVMQRLGAKHVLVVYGMDGMDEVSLGAATQVGELRDGEVREYEIHPEDFGMQMVSNRTLKVADA 272
                                                  ****************************************************************** PP

                                    TIGR01245 265 eenaellkevlegkekkakrdivvlNaaaalyvagkakdlkegvelakeaiksgkalekleelva 329
                                                   e+ ++l e+l +k  + +r+iv lNa++aly a++a+++++g+ela+eai sgka +k++el++
  lcl|FitnessBrowser__Burk376:H281DRAFT_05713 273 TESKAMLLEALDNKP-GVAREIVTLNAGTALYSANVASSIANGIELAREAIASGKARAKVDELIR 336
                                                  **************9.778*****************************************99986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (330 nodes)
Target sequences:                          1  (343 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00
# Mc/sec: 11.50
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer
changes to Amino acid biosynthesis since the publication.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for Amino acid biosynthesis